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Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex with paxillin LD1 motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VZC PDB ENTRY 2VZC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20% (W/V) PEG 10000, 0.1M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.123 α = 90 b = 37.503 β = 90.33 c = 70.244 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD MIRRORS 2006-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 30.03 98.5 0.05 16.4 2.9 20260 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 99.4 0.45 2.5 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VZC 2.1 28.64 19208 1039 98.3 0.219 0.217 0.209 0.255 0.2423 RANDOM 43.1
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.58 -0.86 1.36 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.885 r_dihedral_angle_4_deg 17.106 r_dihedral_angle_3_deg 13.908 r_dihedral_angle_1_deg 7.964 r_angle_refined_deg 1.13 r_scangle_it 0.484 r_mcangle_it 0.361 r_scbond_it 0.324 r_nbtor_refined 0.294 r_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.885 r_dihedral_angle_4_deg 17.106 r_dihedral_angle_3_deg 13.908 r_dihedral_angle_1_deg 7.964 r_angle_refined_deg 1.13 r_scangle_it 0.484 r_mcangle_it 0.361 r_scbond_it 0.324 r_nbtor_refined 0.294 r_nbd_refined 0.213 r_mcbond_it 0.204 r_symmetry_hbond_refined 0.18 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.089 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2262 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing